Example

An example set of input sequences (for Hepatitis B virus) is included in the distribution. To run the example, do the following:

> cd EXAMPLE1
> ./run_mlrgd hbv

(Note that a few of the parameters in EXAMPLE1/run_mlrgd differ from those in the default run_mlrgd - e.g. the circular genome option is switched on.)

The programme produces a number of output files, which will be described in more detail below. The file hbv.fcm.eps (Figure 1; postscript image; view with e.g. ggv hbv.fcm.eps) shows a number of statistics and conservation plots (running mean) for non-coding positions, 1st, 2nd and 3rd codon positions, four-fold degenerate neutral sites, and all nucleotide positions. There are other tracks for the estimated $p$-values, the number of contributing sequences in each column (i.e. not gapped in the alignment), annotated CDSs, and any other annotated features (here the annotated features are from Smith et al. 1998, Moolla et al. 2002, Chen et al. 2005, and the NCBI reference sequence NC_003977).

There is another example (Barley Yellow Dwarf Virus), using GENBANK-format sequences, in EXAMPLE2:

> cd EXAMPLE2
> ./run_mlrgd bydv

In general the command is

> ./run_mlrgd prefix

Figure 1: One of the output plots for Hepatitis B Virus example.